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Opened 10 months ago
Closed 10 months ago
#16599 closed defect (duplicate)
Crash in python_instances_of_class
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001dd3b5ec0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 162 in copy
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py", line 65 in combine_cmd
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)
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"procLaunch" : "2025-01-10 08:49:03.9448 +0800",
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"codeSigningTeamID" : "LWV8X224YF",
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"exception" : {"codes":"0x0000000000000001, 0x00000000006365bd","rawCodes":[1,6514109],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000006365bd"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":54151},
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===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-
> GP49-GP58-GP59-GP60-GP61-2_74A/Baseplate-coot-1-ACEG.pdb"
Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein
Purification/New Phage Proteins/Structure/CryoEM/cryosparc/Corndog
/Baseplate/CornDog-Baseplate-GP49-GP58-GP59-GP60-GP61-2_74A/Baseplate-
coot-1-ACEG.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER M 20 PHE M 22 1 3
Start residue of secondary structure not found: HELIX 2 2 GLY M 38 THR M 41 1
4
Start residue of secondary structure not found: HELIX 3 3 PRO M 142 ARG M 148
1 7
Start residue of secondary structure not found: HELIX 4 4 GLU M 262 ILE M 267
1 6
Start residue of secondary structure not found: HELIX 5 5 SER N 20 PHE N 22 1
3
381 messages similar to the above omitted
End residue of secondary structure not found: HELIX 3 3 PRO M 142 ARG M 148 1
7
Start residue of secondary structure not found: HELIX 4 4 GLU M 262 ILE M 267
1 6
Start residue of secondary structure not found: HELIX 5 5 SER N 20 PHE N 22 1
3
Start residue of secondary structure not found: HELIX 6 6 GLY N 38 THR N 41 1
4
End residue of secondary structure not found: HELIX 7 7 PRO N 142 ARG N 148 1
7
Start residue of secondary structure not found: HELIX 8 8 GLU N 262 ILE N 267
1 6
Start residue of secondary structure not found: HELIX 9 9 SER O 20 PHE O 22 1
3
Start residue of secondary structure not found: HELIX 10 10 GLY O 38 THR O 41
1 4
End residue of secondary structure not found: HELIX 11 11 PRO O 142 ARG O 148
1 7
Start residue of secondary structure not found: HELIX 12 12 GLU O 262 ILE O
267 1 6
Start residue of secondary structure not found: HELIX 13 13 SER P 20 PHE P 22
1 3
Start residue of secondary structure not found: HELIX 14 14 GLY P 38 THR P 41
1 4
End residue of secondary structure not found: HELIX 15 15 PRO P 142 ARG P 148
1 7
Start residue of secondary structure not found: HELIX 16 16 GLU P 262 ILE P
267 1 6
Start residue of secondary structure not found: HELIX 17 17 SER Q 20 PHE Q 22
1 3
Start residue of secondary structure not found: HELIX 18 18 GLY Q 38 THR Q 41
1 4
End residue of secondary structure not found: HELIX 19 19 PRO Q 142 ARG Q 148
1 7
Start residue of secondary structure not found: HELIX 20 20 GLU Q 262 ILE Q
267 1 6
Start residue of secondary structure not found: HELIX 21 21 SER R 20 PHE R 22
1 3
Start residue of secondary structure not found: HELIX 22 22 GLY R 38 THR R 41
1 4
End residue of secondary structure not found: HELIX 23 23 PRO R 142 ARG R 148
1 7
Start residue of secondary structure not found: HELIX 24 24 GLU R 262 ILE R
267 1 6
Start residue of secondary structure not found: HELIX 25 25 SER A 20 PHE A 22
1 3
Start residue of secondary structure not found: HELIX 26 26 GLY A 38 THR A 41
1 4
End residue of secondary structure not found: HELIX 27 27 PRO A 142 ARG A 148
1 7
Start residue of secondary structure not found: HELIX 28 28 GLU A 262 ILE A
267 1 6
Start residue of secondary structure not found: HELIX 29 29 SER C 20 PHE C 22
1 3
Start residue of secondary structure not found: HELIX 30 30 GLY C 38 THR C 41
1 4
End residue of secondary structure not found: HELIX 31 31 PRO C 142 ARG C 148
1 7
Start residue of secondary structure not found: HELIX 32 32 GLU C 262 ILE C
267 1 6
Start residue of secondary structure not found: HELIX 33 33 SER E 20 PHE E 22
1 3
Start residue of secondary structure not found: HELIX 34 34 GLY E 38 THR E 41
1 4
End residue of secondary structure not found: HELIX 35 35 PRO E 142 ARG E 148
1 7
Start residue of secondary structure not found: HELIX 36 36 GLU E 262 ILE E
267 1 6
Start residue of secondary structure not found: HELIX 37 37 SER G 20 PHE G 22
1 3
Start residue of secondary structure not found: HELIX 38 38 GLY G 38 THR G 41
1 4
End residue of secondary structure not found: HELIX 39 39 PRO G 142 ARG G 148
1 7
Start residue of secondary structure not found: HELIX 40 40 GLU G 262 ILE G
267 1 6
Start residue of secondary structure not found: HELIX 41 41 SER I 20 PHE I 22
1 3
Start residue of secondary structure not found: HELIX 42 42 GLY I 38 THR I 41
1 4
End residue of secondary structure not found: HELIX 43 43 PRO I 142 ARG I 148
1 7
Start residue of secondary structure not found: HELIX 44 44 GLU I 262 ILE I
267 1 6
Start residue of secondary structure not found: HELIX 45 45 SER K 20 PHE K 22
1 3
Start residue of secondary structure not found: HELIX 46 46 GLY K 38 THR K 41
1 4
End residue of secondary structure not found: HELIX 47 47 PRO K 142 ARG K 148
1 7
Start residue of secondary structure not found: HELIX 48 48 GLU K 262 ILE K
267 1 6
Start residue of secondary structure not found: SHEET 1 1 1 ALA M 29 ASP M 35
0
Start residue of secondary structure not found: SHEET 2 2 2 HIS M 72 VAL M 75
0
Start residue of secondary structure not found: SHEET 3 3 3 ASP M 78 THR M 81
0
Start residue of secondary structure not found: SHEET 4 4 4 GLU M 102 GLN M
112 0
263 messages similar to the above omitted
End residue of secondary structure not found: SHEET 76 7676 GLU A 102 GLN A
112 0
Start residue of secondary structure not found: SHEET 77 7777 ASP A 122 PHE A
134 0
Start residue of secondary structure not found: SHEET 78 7878 GLY A 171 PRO A
175 0
Start residue of secondary structure not found: SHEET 79 7979 TYR A 183 LYS A
193 0
Start residue of secondary structure not found: SHEET 80 8080 LYS A 196 TYR A
204 0
Start residue of secondary structure not found: SHEET 81 8181 CYS A 207 ILE A
212 0
6 messages similar to the above omitted
End residue of secondary structure not found: SHEET 88 8888 GLU C 102 GLN C
112 0
Start residue of secondary structure not found: SHEET 89 8989 ASP C 122 PHE C
134 0
Start residue of secondary structure not found: SHEET 90 9090 GLY C 171 PRO C
175 0
Start residue of secondary structure not found: SHEET 91 9191 TYR C 183 LYS C
193 0
Start residue of secondary structure not found: SHEET 92 9292 LYS C 196 TYR C
204 0
Start residue of secondary structure not found: SHEET 93 9393 CYS C 207 ILE C
212 0
51 messages similar to the above omitted
Chain information for Baseplate-coot-1-ACEG.pdb
---
Chain | Description
1.1/A 1.1/C 1.1/E 1.1/G 1.1/I 1.1/K 1.1/M 1.1/N 1.1/O 1.1/P 1.1/Q 1.1/R | No description available
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F | No description available
1.3/A 1.3/B 1.3/C | No description available
1.4/A 1.4/B 1.4/D 1.4/E 1.4/F 1.4/G 1.4/H 1.4/I 1.4/J 1.4/K 1.4/L 1.4/M | No description available
1.5/A 1.5/B 1.5/C | No description available
1.4/C 1.4/N 1.4/O 1.4/P 1.4/Q 1.4/R | No description available
Already setting window visible!
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/ChimeraX/Cluster
> O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb"
Chain information for
Corndog_61_Trimer_1cf1e_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb
#2
---
Chain | Description
A B C | No description available
> select add #2
18573 atoms, 18993 bonds, 2508 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 to #1.5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with
Corndog_61_Trimer_1cf1e_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#2), sequence alignment score = 495.4
RMSD between 59 pruned atom pairs is 1.307 angstroms; (across all 101 pairs:
18.071)
> select subtract #2
Nothing selected
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/ChimeraX/Cluster
> O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb"
> "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/ChimeraX/Cluster
> O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb"
> "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/ChimeraX/Cluster
> O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb"
> "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/ChimeraX/Cluster
> O/Corndog_61/Corndog_61_Trimer/Corndog_61_Trimer_1cf1e_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb"
Chain information for
Corndog_61_Trimer_1cf1e_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb
#3
---
Chain | Description
A B C | No description available
Chain information for
Corndog_61_Trimer_1cf1e_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb
#4
---
Chain | Description
A B C | No description available
Chain information for
Corndog_61_Trimer_1cf1e_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb
#5
---
Chain | Description
A B C | No description available
Chain information for
Corndog_61_Trimer_1cf1e_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb
#6
---
Chain | Description
A B C | No description available
> ui tool show Matchmaker
> matchmaker #2-6 to #1.5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with
Corndog_61_Trimer_1cf1e_unrelaxed_rank_001_alphafold2_multimer_v3_model_4_seed_000.pdb,
chain B (#2), sequence alignment score = 495.4
RMSD between 59 pruned atom pairs is 1.307 angstroms; (across all 101 pairs:
18.071)
Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with
Corndog_61_Trimer_1cf1e_unrelaxed_rank_002_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#3), sequence alignment score = 490.6
RMSD between 61 pruned atom pairs is 1.305 angstroms; (across all 101 pairs:
26.184)
Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with
Corndog_61_Trimer_1cf1e_unrelaxed_rank_003_alphafold2_multimer_v3_model_2_seed_000.pdb,
chain C (#4), sequence alignment score = 503.8
RMSD between 35 pruned atom pairs is 0.895 angstroms; (across all 101 pairs:
31.569)
Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with
Corndog_61_Trimer_1cf1e_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb,
chain A (#5), sequence alignment score = 505
RMSD between 40 pruned atom pairs is 0.977 angstroms; (across all 101 pairs:
23.986)
Matchmaker Baseplate-coot-1-ACEG.pdb, chain A (#1.5) with
Corndog_61_Trimer_1cf1e_unrelaxed_rank_005_alphafold2_multimer_v3_model_3_seed_000.pdb,
chain A (#6), sequence alignment score = 496.6
RMSD between 59 pruned atom pairs is 1.224 angstroms; (across all 101 pairs:
14.362)
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #2 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> close #5-6
> show #4 models
> show #3 models
> show #2 models
> close #2-3
> rename #4 Corndog_61
> select add #4
18573 atoms, 18993 bonds, 2508 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.67349,0.26764,-0.68905,276.61,-0.72435,-0.42485,0.54298,277.3,-0.14742,0.8648,0.47999,79.851
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-
> GP49-GP58-GP59-GP60-GP61-2_74A/cryosparc_P2_J280_008_volume_map_sharp.mrc"
Opened cryosparc_P2_J280_008_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.06, shown at level 0.227, step 2, values float32
> surface dust #2 size 10.6
> volume #2 level 0.3
> volume #2 step 1
> transparency 50
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-
> GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer.pdb" models #4 selectedOnly
> true relModel #2
> ui tool show "Fit in Map"
> fitmap #4 inMap #2
Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc
(#2) using 18573 atoms
average map value = 0.08724, steps = 2000
shifted from previous position = 1.69
rotated from previous position = 4.84 degrees
atoms outside contour = 17484, contour level = 0.3
Position of Corndog_61 (#4) relative to
cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.61456329 0.31006657 -0.72537624 276.06442658
-0.77933139 -0.38117747 0.49733924 275.04870896
-0.12228881 0.87095491 0.47590229 79.79110445
Axis 0.28738893 -0.46390091 -0.83797586
Axis point 200.56043122 47.30830227 0.00000000
Rotation angle (degrees) 139.45707837
Shift along axis -115.12050621
> hide #1.5 models
> hide #1.4 models
> hide #1.3 models
> hide #1.2 models
> hide #1.1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1.5/A #1.5/B #1.5/C
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A #4/B #4/C
Alignment identifier is 2
Already setting window visible!
> select #1.5/A-C:6
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #1.5/A-C:6-11
150 atoms, 156 bonds, 18 residues, 1 model selected
> select #4/A-C:5-6
39 atoms, 36 bonds, 6 residues, 1 model selected
> select #4/A-C:1-6
132 atoms, 132 bonds, 18 residues, 1 model selected
> select #4/A-C:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #4/A-C:1-5
120 atoms, 120 bonds, 15 residues, 1 model selected
> delete sel
> select #1.5/A-C:106
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1.5/A-C
2376 atoms, 2427 bonds, 303 residues, 1 model selected
> select sequence
> GEIPDWVRNVPRQVRKLPPNNQWEGISEEMMQQLRGQLLESILSAVVQAIRGLFVPGPFGSAAEQLEQWAQGLGAEIIAKIYELTGIDLSSWDAFLESLSD
4752 atoms, 4854 bonds, 606 residues, 2 models selected
> select clear
> select add #4
18453 atoms, 18870 bonds, 2493 residues, 1 model selected
> view matrix models
> #4,-0.65768,0.28234,-0.69838,276.79,-0.74308,-0.39535,0.53994,274.81,-0.12366,0.87406,0.46981,79.774
> view matrix models
> #4,-0.65768,0.28234,-0.69838,276.99,-0.74308,-0.39535,0.53994,274.67,-0.12366,0.87406,0.46981,81.796
> fitmap #4 inMap #2
Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc
(#2) using 18453 atoms
average map value = 0.08765, steps = 2000
shifted from previous position = 4.36
rotated from previous position = 2.85 degrees
atoms outside contour = 17356, contour level = 0.3
Position of Corndog_61 (#4) relative to
cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.62528913 0.29253997 -0.72348729 278.24689192
-0.76616580 -0.40634170 0.49787186 279.27516578
-0.14833564 0.86562509 0.47821517 80.13241653
Axis 0.29193203 -0.45657027 -0.84042804
Axis point 201.00137478 52.18998333 -0.00000000
Rotation angle (degrees) 140.96012791
Shift along axis -113.62508686
> fitmap #4 inMap #2
Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc
(#2) using 18453 atoms
average map value = 0.08681, steps = 2000
shifted from previous position = 5.1
rotated from previous position = 1.98 degrees
atoms outside contour = 17365, contour level = 0.3
Position of Corndog_61 (#4) relative to
cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.62899903 0.32224368 -0.70747383 272.37984974
-0.76611149 -0.41150227 0.49369937 280.61671488
-0.13203559 0.85254026 0.50570912 79.99967427
Axis 0.27983143 -0.44873845 -0.84872150
Axis point 198.07337970 53.91316297 0.00000000
Rotation angle (degrees) 140.12063271
Shift along axis -117.60051061
> view matrix models
> #4,-0.629,0.32224,-0.70747,272.84,-0.76611,-0.4115,0.4937,279.79,-0.13204,0.85254,0.50571,80.672
> fitmap #4 inMap #2
Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc
(#2) using 18453 atoms
average map value = 0.08713, steps = 2000
shifted from previous position = 6.06
rotated from previous position = 2.58 degrees
atoms outside contour = 17392, contour level = 0.3
Position of Corndog_61 (#4) relative to
cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.62461800 0.30414044 -0.71927112 276.08488128
-0.77233484 -0.37686456 0.51134333 273.37549885
-0.11554761 0.87491239 0.47029465 79.74838108
Axis 0.28257069 -0.46922190 -0.83665083
Axis point 199.08540406 47.00859691 0.00000000
Rotation angle (degrees) 139.95986232
Shift along axis -116.98182556
> fitmap #4 inMap #2
Fit molecule Corndog_61 (#4) to map cryosparc_P2_J280_008_volume_map_sharp.mrc
(#2) using 18453 atoms
average map value = 0.08799, steps = 2000
shifted from previous position = 5.9
rotated from previous position = 2.24 degrees
atoms outside contour = 17350, contour level = 0.3
Position of Corndog_61 (#4) relative to
cryosparc_P2_J280_008_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.62636364 0.30559819 -0.71713202 275.76138126
-0.76611507 -0.41126712 0.49388972 280.30588585
-0.14400102 0.85876021 0.49172615 79.96047476
Axis 0.28754225 -0.45166541 -0.84458144
Axis point 199.88715672 53.35489490 0.00000000
Rotation angle (degrees) 140.61974856
Shift along axis -114.84455684
> select subtract #4
Nothing selected
> hide #4 models
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-
> GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-coot-0.pdb"
Chain information for Corndog_61_Trimer-coot-0.pdb #3
---
Chain | Description
A B C | No description available
> select #4/A-C:6
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #4/A-C:6-9
84 atoms, 84 bonds, 12 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/A:6-11
50 atoms, 52 bonds, 6 residues, 1 model selected
> view clip false
> select #4/A:12-13
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #4/A:12-18
60 atoms, 60 bonds, 7 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:6
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:6-13
68 atoms, 70 bonds, 8 residues, 1 model selected
> view clip false
> select #3/A:61
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:61-68
49 atoms, 51 bonds, 8 residues, 1 model selected
> hide #3 models
> show #1.5 models
> select #1.5/A-C:6
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #1.5/A-C:6-12
171 atoms, 177 bonds, 21 residues, 1 model selected
> show #3 models
> select #3/A:56
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:56-60
41 atoms, 41 bonds, 5 residues, 1 model selected
> select #3/A:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:48-52
33 atoms, 32 bonds, 5 residues, 1 model selected
> select #3/A:41-42
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3/A:41-44
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #3/A:35
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:35-37
25 atoms, 24 bonds, 3 residues, 1 model selected
> select #3/A:30-31
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3/A:30-32
18 atoms, 17 bonds, 3 residues, 1 model selected
> view matrix models #3,1,0,0,0.68894,0,1,0,-0.99432,0,0,1,-1.7586
> undo
> close #3
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-
> GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-coot-1.pdb"
Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein
Purification/New Phage Proteins/Structure/CryoEM/cryosparc/Corndog
/Baseplate/CornDog-Baseplate-GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-
coot-1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 10 ARG A 13 1 4
Start residue of secondary structure not found: HELIX 2 2 GLN A 27 GLU A 29 1
3
Chain information for Corndog_61_Trimer-coot-1.pdb #3
---
Chain | Description
A B C | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:777-836
435 atoms, 441 bonds, 60 residues, 1 model selected
> select #3/A
5944 atoms, 6075 bonds, 807 residues, 1 model selected
> save "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-
> GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-coot-2.pdb" models #3
> selectedOnly true relModel #2
> select #3/A:30
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:30
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.5/A-C:10-13,33-55,66-89,97-104
1416 atoms, 1428 bonds, 177 residues, 1 model selected
> view matrix models #1.5,1,0,0,0.5085,0,1,0,-1.2452,0,0,1,-1.608
> undo
> select clear
> close #3
> open "/Users/melvinshen/Desktop/Sinica /Protein Purification/New Phage
> Proteins/Structure/CryoEM/cryosparc/Corndog /Baseplate/CornDog-Baseplate-
> GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-coot-3.pdb"
Summary of feedback from opening /Users/melvinshen/Desktop/Sinica /Protein
Purification/New Phage Proteins/Structure/CryoEM/cryosparc/Corndog
/Baseplate/CornDog-Baseplate-GP49-GP58-GP59-GP60-GP61-2_74A/Corndog_61_Trimer-
coot-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 24 24 GLU B 33 ARG B 56 1 24
Start residue of secondary structure not found: HELIX 25 25 ALA B 67 GLN B 76
1 10
Start residue of secondary structure not found: HELIX 26 26 LEU B 78 THR B 90
1 13
Start residue of secondary structure not found: HELIX 27 27 TRP B 97 LEU B 101
1 5
Start residue of secondary structure not found: HELIX 28 28 GLU B 102 SER B
105 1 4
121 messages similar to the above omitted
Chain information for Corndog_61_Trimer-coot-3.pdb #3
---
Chain | Description
A | No description available
> view orient
> ui mousemode right "map eraser"
> volume erase #2 center 299.53,293.01,461.09 radius 107.6
Opened cryosparc_P2_J280_008_volume_map_sharp.mrc copy as #6, grid size
512,512,512, pixel 1.06, shown at step 1, values float32
> surface dust #6 size 10.6
> volume erase #6 center 294.08,290.18,421.18 radius 107.56
> set bgColor white
> set bgColor black
> close #5
Cell requested for row 3 is out of bounds for table with 10 rows! Resizing
table model.
> close #4
> combine #3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U0000PTA/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1 (23B74)
Kernel Version: Darwin 23.1.0
Time since boot: 14 days, 21 hours, 48 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.14.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.1.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.16
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.3
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.5
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.56
ChimeraX-AtomicLibrary: 14.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202403220040
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.3
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.37.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.9
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.1
fonttools: 4.50.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.10.0
html2text: 2024.2.26
idna: 3.6
ihm: 0.43
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
Jinja2: 3.1.3
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.1.0
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.3
matplotlib-inline: 0.1.6
MolecularDynamicsViewer: 1.6
msgpack: 1.0.8
ndindex: 1.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.2.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.9.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.3
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.2.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.0
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.3.0
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3302
pyparsing: 3.1.2
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.2
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 25.1.2
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.12.0
setuptools: 69.2.0
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.0
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.1
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.1
typing-extensions: 4.10.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (2)
comment:1 by , 10 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in python_instances_of_class |
comment:2 by , 10 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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